Inter-satellite link is a critical technology for the satellite navigation system to realize its independent running. On the base of Walker(24/3/2) constellation, the visibilities between satellites and relative constraints of inter-satellite links were analyzed. After computing and determining the arrange scheme of satellites on the same orbit, the method to establish inter-satellite link topology with the minimal position dilution of precision(PDOP) value, that means the ranging precision is highest, was probed. On this basis the optimal paths between satellites and between satellites and ground stations were computed using Dijkstra algorithm. The statistics of time-delay in inter-satellite data transmission and data flow of satellite nodes show this link generation method can fulfill the pre-defined technological requirements and is practicable. Meanwhile simulate on three different strategies that are shortest path, minimal hop and balanced flow to verify the different results of the strategies.